Works for reads as short as 30 bp where other methods
fail. You don't have to distort your data through a
non-linear filter like assembly just to get results. Linear
and broad diagnostics enables
ecological management strategies
for tough problems.

Phylogenetic signature algorithm works for
novel organisms, so you're not
blind to microbes
that aren't similar to those in genome databases. More
sensitive to distant relationships than methods based on
mapping methods.

We already built a Tree of Life for you, so your
analysis doesn't have to wait on
a team of bioinformaticians to finish their
analysis first.

Who's there? A bunch of viruses!
Viral metagenomes from a set of patients with diarrhea. It looks like the
cause of their illness was an enterovirus. Data
courtesy
Dr. Charles Chiu, UCSF.

What are those algae doing?
Sequedex output from a series of algal
transcriptomes under various treatments. The organism
under study here, Chlorella, has no reference genome or
transcriptome. Data courtesy
Dick Sayre, LANL.

Complex communities, simple differences:
People who have tooth decay show huge differences (>40
sigmas) in the frequency of genes that let bacteria live
off sugars instead of nucleic acids. Blue dots are
increased in caries, red is decreased. Data from NCBI SRA
study SRP007831

Tissue differentiation by transcriptomes.
Data from the
MPSS
atlas of human gene expression

A computer with a 64-bit operating
system such as Mac Snow Leopard or later or
Linux 2.6 or later.

A 64-bit Java 1.7 or later run-time
installed. The Java 1.6 distributed with Mac OS X is not
acceptable. Desktop users may download Java
from the java.com website.

A 64-bit Python 2 distribution with working SciPy installed (2.5 or later, but tested under 2.7). The python distributed with Mac OS X
10.9.2 (Mavericks) or later is acceptable; we recommend that you upgrade to the latest OS, but if you cannot do this for some reason you can install a 3rd-party python distribution.
Desktop users may download a free and complete python distribution
(Anaconda)
here. Windows users must install Anaconda in the default system location.

1 GB of disk space is required for download,
installation, and testing.

4 GB of RAM. However, RAM is cheap and
Sequedex will use bigger data modules that identify more reads if you have
8, 16, 32, or 48 GB installed.

A windowing environment even on server systems
to run the licensing GUI.

Make sure you have satisfied the System Requirements listed in the tab above
before doing any further steps. Mac users will need to download Java and python
as listed there, as the OSX-provided versions will not work.

Download the Sequedex distribution using the button at the right, and move the
downloaded archive file to the directory where you wish to install Sequedex.

For now, installation is by command line on all platforms. Open a new command-line
window (since an old one may not have the new java and python on the path) and issue the
following commands, replacing the items in angle brackets with appropriate values
for your system:
% cd <path to sequedex-archive>
% tar xzf sequedex-<version>-<platform>.tgz
% cd sequedex
If your network is behind a proxy server, do the following:
% bin/sequedex-config http_proxy <your proxy>
% bin/sequedex-config https_proxy <your proxy>
% bin/sequedex-config no_proxy <mycompany.com>,localhost,127.0.0.1
Then check to see if your system can benefit from an update:
% bin/sequedex-changes
If the output of that command indicates you should update, do the following:
% bin/sequedex-bootstrap
% bin/sequedex-update

Sequedex is now installed. If you wish, you may add the bin/
directory to your path for convenience.

You may obtain a free 6-month node-locked demo license by
submtting a license information file by e-mail. A demo
license will be returned to you immediately if one has
not been granted for your e-mail or node ID before.
Terms of the demo license are available
here.

To create a license information file, start the Sequedex
GUI and click on "Utilities->Request license". Follow
the instructions to generate a license information file.

Free demo licenses are available for a 6-month period by
e-mailing the license information file as an attachment to
sequedex-demo-license@lanl.gov. A license file
will be returned to you at the e-mail address
you specified in the license information file.

One-year paid licenses are available at the special
introductory rate of 1000 USD for academic users by
contacting
sequedex-license@lanl.gov.

Once you have obtained a demo license, you may wish to test that
everything is working properly. A set of test data has
been provided for this purpose
here (tar)
or
here (zip).
Unpack the data, start sequescan, and click on the file chooser icon at the
right edge of the Input line. In the directory you unpacked the test files,
select the sequedex.testdata directory. Then click the "Run Sequescan" button.
If you have not previously accepted the license, you
will have to accept it, and click "Run Sequescan" again. Sequedex should return results
indicating success within about 3 minutes. Click on on the "Run Sequinator" button
to display the results.